Wiggle
Wiggle (keyboard shortcut "w") automatically seeks better backbone and sidechain positions. Wiggle can work on both the backbone and the sidechains at the same time, or backbone and sidechains can be wiggled separately. There are two different types of wiggle: regular wiggle and local wiggle, which produce different results. Wiggle does not change the backbone of locked or frozen segments, but it may change the position of any unlocked or unfrozen sidechains. Wiggle is affected by the wiggle power setting. Lower wiggle power means faster wiggles, but less precise results. Wiggle and shake are the most basic automatic tools in Foldit. Unlike shake, wiggle requires a variable number of cycles, as seen in the counter section of the timer/counter in the upper left. Unlike shake, wiggle can change the shape of the backbone. If there are large clashes or other problems, wiggle can cause the protein to fly apart. Various techniques, including freezing and banding, can be used to help prevent drastic changes during a wiggle. A wiggle can be either global or local. A global wiggle affects the backbone and/or sidechains of the entire protein. A local wiggle affects only a portion of the protein. Local wiggle works differently than a global wiggle. In the original interface, any wiggle started using the Actions menu or using a keyboard shortcut is global. Right-clicking (or control-clicking) on a segment and selecting "Wiggle" from the wheel menu performs a local wiggle of the backbone and sidechains within the same secondary structure and adjacent loops. For example, if you right-click a segment of a sheet and select "Wiggle", the backbone and sidechains of all the segments in that sheet, and the segments in adjacent loops are wiggled. In this type of local wiggle, there is no way to wiggle the backbone and sidechains separately in the original interface. In the selection interface, if nothing is selected, the wiggle tools perform a global wiggle. The icons for the wiggle tools contain the word "all" in this case. If segments are selected, the wiggle tools affect only those segments. There is no way to perform a local wiggle manually in the selection interface, but local wiggle is still available via recipes. See the local wiggle article for more on local wiggle. The keyboard shortcuts for the "Wiggle Backbone" tool are different in the original and selection interfaces. The shortcuts are: Recipe interfaces Wiggle and local wiggle are separate at the recipe level. In GUI recipes, the command "Wiggle" is available. (In contrast, there's a a separate "Local Wiggle Sequence" command.) The Wiggle command has the usual segment selection options for a GUI recipe: "all", "by stride", or "user pick". There is no option to wiggle just the backbone or the sidechains. In version 1 of the Foldit Lua interface, there are three separate global wiggle functions: *do_global_wiggle_all *do_global_wiggle_sidechains *do_global_wiggle_backbone These functions honor selections, so with nothing selected (or everything selected), they're equivalent of structure.WiggleAll. In version 2 of the Foldit Lua interface, the functions structure.WiggleAll and structure.WiggleSelected are available. Both functions accept arguments that control whether the backbone and the sidechains are wiggled. Category:Tools Category:Glossary